Wydział Chemii

Oleg V. Shishkin

Przemysław Dopieralski

G. V. Palamarchuk

Zdzisław Latajka

2010

Chemical Physics Letters

490

221-225

10.1016/j.cplett.2010.03.044

Naukowa

Angielski

Artykuł

Theoretical investigation of the conformation of 2′-deoxyriboadenosine monophosphate protonated at the N7 atom and stabilized by a very strong C8–H⋯O–P hydrogen bond indicates that this hydrogen bond may be disrupted by rotation of the adenine moiety around the glycosidic bond. A B3LYP/aug-cc-pVDZ scan of the relaxed potential energy surface demonstrates that this rotation is a multi-stage process, accompanying proton transfer from the N7 atom of adenine to the oxygen atom of the phosphate group with a change of conformation of the nucleotide from south/anti to north/syn conformation. Car–Parrinello molecular dynamics simulation indicates that rotation around the glycosidic bond is the preferred way for relaxation of the molecular geometry of this conformer. Both processes, i.e. conformational transition and proton transfer, are strongly coupled. However, the conformer containing a strong C–H⋯O hydrogen bond also corresponds to a local minimum on the Gibbs free energy surface. A specific property of this hydrogen bond is the large variation of the H⋯O distance (ranging from 1.3 to 2.2 Å), which is not caused by proton movement between the carbon and oxygen atoms, but rather by relative motions of the adenine and phosphate moieties.

http://dx.doi.org/10.1016/j.cplett.2010.03.044

http://www.elsevier.com